Fluctuating charge, polarizable dipole, and combined models: parameterization from ab initio quantum chemistry

Article Abstract:

A study was conducted to analyze the fluctuating charge, fluctuating dipole and combined models for substituted benzenes. A general linear response framework containing both fluctuating charges and dipoles was formulated. An electrostatic model was then completed by adding fixed charges fit to the zero-field quantum chemical electrostatic potential. Results indicated the accuracy of the many-body response of the peptide models and was in good agreement with ab initio computations of the changes in the electrostatic potential.

Peptides, Electrostatics, Benzene, Quantum chemistry

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Poisson-Boltzmann analytical gradients for molecular modeling calculations

Article Abstract:

A Poisson-Boltzmann (PB) methodology for use with large biomolecules ranging in size from 500 to 5000 atoms. The procedure employs a Gaussian definition of the solvent-accessible surface of the molecule which simplifies the numerical calculations. The solvation energies derived from the Gaussian surface are also similar with those from the Connolly surface. A finite element code, which has been interfaced with the IMPACT molecular program of Levy, is used in deriving the PB energies and gradients.

Models, Molecular structure, Biomolecules

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Generalized born model based on a surface integral formulation

Article Abstract:

Research was conducted to examine the hypothesis that corrections to the surface-area-based version of the generalized Born model (S-GB) can generate substantial improvements in the accuracy of the method compared to accurate Posson-Boltzmann (PB) continuum solvation calculations. The main objective is to reformulate the GB approach in a new analytical context. Energetic comparisons of GB, corrected S-GB and PB for multiple conformations of proteins and peptides are presented.

Evaluation, Transport theory, Poisson's equation

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